Esvald, E.-E. | bioRxiv Science

bioRxiv2026

Direct Mapping of CDK2 Substrates in Embryonic Stem Cells Uncovers an AP-Site Repair Mechanism via HMCES Phosphorylation

Embryonic stem cells (ESCs) proliferate rapidly while robustly maintaining genomic integrity and exhibiting high cell-cycle kinase activity. How this activity contributes to genome integrity remains unclear. Here, using mouse ESCs engineered to express an analog-sensitive CDK2, we combine thiophosphate labeling with mass spectrometry to define a high-confidence CDK2 substrate landscape. We uncovered 65 CDK2 substrates in total, including both known and previously unrecognized substrates. Among these, HMCES, a sensor of apurinic/apyrimidinic (AP) sites, was identified as a specific cyclin E-CDK2 substrate. We mapped three CDK2-dependent phosphorylation sites in HMCES and showed that phosphorylation of these sites decreased HMCES binding to ssDNA. Mutational analysis further revealed that HMCES docks to cyclin E-CDK2 complexes via the hydrophobic patch on cyclin E. Finally, we demonstrated that HMCES phosphorylation contributes to AP-site repair and promotes ESC proliferation. Together, our findings uncover a CDK2-HMCES signaling axis that links rapid cell-cycle progression to the preservation of genome stability in mouse ESCs.

developmental biology↗

bioRxiv2020

Intronic enhancer region governs transcript-specific BDNF expression in neurons

Brain-derived neurotrophic factor (BDNF) controls the survival, growth, and function of neurons both during the development and in the adult nervous system. BDNF gene is transcribed from several distinct promoters generating transcripts with alternative 5 exons. BDNF transcripts initiated at the first cluster of exons have been associated with the regulation of body weight and various aspects of social behavior, but the mechanisms driving the expression of these transcripts have remained poorly understood. Here, we identify an evolutionarily conserved intronic enhancer region inside the BDNF gene that regulates both basal and stimulus-dependent expression of the BDNF transcripts starting from the first cluster of 5 exons in neurons. We further uncover a functional E-box element in the enhancer region, linking the expression of BDNF and various pro-neural basic helix-loop-helix transcription factors. Collectively, our results shed new light on the cell type- and stimulus-specific regulation of the important neurotrophic factor BDNF.

neuroscience↗